Chapter 4: Carbon and the Molecular Diversity of Life(Checked at 9:00 PM 12/11/10. Ch 4 looks fine. Ch 5 only finished through lipids)Functional Groups
Hydroxyl
Carbonyl
Carboxyl
Amino
Sulfydryl
Phosphate
Methyl
Structure
-OH
C=O
-COOH
-NH2
-SH
-OPO3
-CH3
Name of Compounds
Alcohols (usually end in –ol)
Ketones (if the carbonyl group is within a carbon skeleton) Aldehydes (if the carbonyl groups is at the end of the carbon skeleton)
Carboxylic Acids (organic acids)
Amines
Thiols
Organic Phosphates
Methyl
Functional Properties
Polar as a result of the electronegative oxgen atom drawing electrons toward itself Attracts water molecules,helping dissolve organic compounds such as sugars
A ketone and aldehyde may be structural isomers with different properties
Has acidic properties because it is a source of hydrogen ions The covalent bond between oxygen and hydrogen is so polar that hydrogen ions tend to dissociate reversibly
Acts as a base; can pick up a proton from the surrounding solution.
Two sulhydryl groups can interact to help stabilize protein structure
Makes the molecule of which is is a part an anion (negatively charged ion) Can transfer energy between organic molecules
Makes molecules nonpolar
Pictures taken from Campbell Biology Online E-Book
Important Concepts ₪ Organic Chemistry – the study of carbon compounds ₪ Hydrocarbons – Organic moleclues that consist of only carbon and hydrogen atoms ₪ Tetravalence – The carbon completes its valence shell by sharing electrons with other atoms in four covalent bonds. This makes a large, complex molecule possible. ₪ Isomers – Compounds that have the same molecular formula but different structures.Therefore, they have different chemical properties. o Structural Isomers – Molecules that have the same molecular formula but differ inthe covalent arrnagement of atoms o Geometric Isomers – Compounds with the same covalent partnerships that differ in the spatial arrangement of atoms around a carbon-carbon double bond. ₪ Enantiomers – Molecules that are mirror images of each other o Levo-Isomer: Left Handed o Dextra-Isomer: Right Handed ₪ Living matter consists mainly of: Carbon, Oxygen, Hydrogen, Nitrogen, Sulfur, and Phosphorus ₪ Carbon (with its four covalent bonds) is the basiv building block in molecular architecture.
Chapter 5: The Structure and Function of Macromolecules
Overview-The Molecules of Life
- Each type of small molecule has unique properties from the arrangement of their atoms
- The four main classes of large biological molecules are: carbohydrates, lipids, proteins, and nucleic acids
5.1: Most Macromolecules are Polymers, built from Monomers
- Carbohydrates, proteins, and nucleic acids are chain like molecules called polymers
- A polymer is a long molecule with many similar or identical building blocks linked by a covalent bond.
- Smaller building blocks of a polymer is called a monomer
The Synthesis and Breakdown of Polymers
- Monomers are connected by a reaction in which two molecules are covalently bonded to each other through loss of a water molecule called condensation reaction (dehydration reaction) -- the molecule lost is water
- When a bond forms between two monomers each monomer contributes part of the water molecule that is lost--hydroxyl group (-OH) and hydrogen (-H)
- This process is repeated to form a polymer
- Cell must expend energy to have dehydration reactions and with the help of enzymes
- Polymers are broken down to monomers by hydrolysis - this process is essentially the reverse of dehydration reaction -- means to break with water
- Bonds between monomers are broken down by the addition of water molecules -- a hydrogen from the water attaching to one monomer and a hydroxyl group attaching to the adjacent monomer (Ex. digestion in our bodies)
The Diversity of Polymers
- Each cell has thousands of kinds of macromolecules -- varies between types of cells
- Difference between human siblings is in the variation in polymers -- DNA and proteins
- Monomers are constructed from 40-50 common monomers (Ex. proteins are made up of 20 different amino acids in a chain)
- Small molecules common to all organisms are ordered into unique macromolecules
5.2: Carbohydrates Serve as Fuel and Building Material
- Carbohydrates: include both sugars and polymers of sugars
- The simplest carbohydrates are monosaccharides (simple sugars) -- Disaccharides are double sugars -- two monosaccharides joined by condensation reaction
Sugars
- Monosaccharides have some multiple of unit CH2O
- Glucose is the most common monosaccharide -- central importance to the chemistry of life (know other examples such as fructose and galactose - not structure but names) - Molecule has carbonyl group and multiple hydroxyl groups
- Glucose has ring formed - Know this
(from Figure 5.4 on Online Website)
Figure 5.4
- Monosaccharides are a major nutrient for cells
- Cellular respiration is when cells extract energy from glucose molecules
- Disaccharide is two monosaccharides joined by a glycosidic linkage - a covalent bond formed between two monosaccharides by dehydration reaction (sugar is a disaccharide-sucrose-with two monomers of glucose and fructose)
- Plants transport carbohydrates from leaves to roots
- Lactose is the sugar present in milk and is a disaccharide - Polysaccharide are macromolecules with hundreds of monosaccharides jointed with glycosidic linkages.
- They serve as storage materials and building materials for structures that protect the cell and organisms
- Starch is a storage polysaccharide of plants- it is a polymer consisitng of entirely glucose monomers.
- Plants store starch within their chloroplast - it serves as cellular fuel and represents stored energy
- Animals store polysaccharides called glycogen- it is a polymer of glucose - stored mainly in the liver and muscle cells - hydrolysis of glycogen in these cells releases glucose when there is a demand for sugar
- Organisms build strong materials from structural polysaccharides - like cellulose - a major component of plant cell walls
- Cellulose is a polymer of glucose but has different glycosidic linkages
- Cellulose has a three dimensional shape but starh has a helical shape - cellulose is straight and never branches
- Many organisms do not have the enzyme needed to digest cellulose - humans do not - the cellulose passes through the digestive tract and is eliminated - the cellulose abrades the wall of the digestive tract and helps food pass through smoothly
- Chitin the carbohydrate used by arthropods to build their exoskeletons - hard case that surrounds the softer parts of an animal
- Chitin is similar to cellulose - the glucose monomer of chitin has a nitrogen-containing appendage.
5.3: Lipids are a Diverse Group of Hydrophobic Molecules
- Lipids are the molecules that do not consist of polymers
- Lipids are grouped together because they share one important shape: they have little to no affinity to water - hydrophobic - may have some polar bonds but most of lipids consist of hydrocarbons
- Fats are large molecules assembled from smaller molecules by dehydration reaction - constructed of glycerol and fatty acids
- A fatty acid has a long carbon skeleton (16-18 carbon atoms) - one end of fatty acid is carboxyl group (funtional group) - hydrocarbon chain is attached to carboxyl group ( reason it is hydrophobic)
Figure 5.11
(From Online Textbook-Figure 5.11)
- To make a fat three fatty acid molecules bind to glycerol by ester linakge (bond between a hydroxyl group and a carboxyl group) resulting fat is a triacylglycerol
- Fatty acids vary in length and location of the double bonds
- There are saturated and unsaturated fats - refers to the structure of the hydrocarbon chains of the fatty acids
- Saturated Fatty Acid - no double bonds between carbon atoms composing the chain - as many hydrogen atoms as possible bind to skeleton
- Unsaturated Fatty Acid - one or more double bond - formed by the removal of hydrogen atoms from teh carbon skeleton
Figure 5.12
(From Online Book - Figure 5.12)
- Most animal fats are saturated - lard and butter - solid at room temperature
- Plants and fish fats are unsaturated - liquid at room temperature - oils
- Saturated fats in excess in diet leads to cardiovascular diseases - atherosclerosis - build up impedes blood flow in blood vessels
- Major function of fats is energy storage - stores more than polysaccharides (starch) - useful for animals since they must carry their stored energy
- Phospolipid - similar to a fat - has only two fatty acids attached to a glycerol (instead of three)
- Hydrocarbon tails are hydrophobic and heads are hydrophilic - bilayer as boundry between cell and the external enviroment
- Steroids are lipids characterized by a carbon skeleton with four fused rings
- Cholesterol is a type of steroid that is common in animal cell membranes - crucial molecule in animals - synthesizes sex hormones
Figure 5.15
(Figure 5.15 from Online Textbook)
Chapter 5
organization is the key to life protein- consists of one or more polypeptides folded and coiled into a specific conformation (end in –ase)
Protein Structure - all proteins are constructed from the same set of 20 amino acid monomers, but The shape determines the function - Amino Acids- organic molecules with both carboxyl and amino groups · at the center is the alpha carbon with 4 components attached 1.
See full size image
hydrogen adam 2. carboxyl group 3. amino group 4. variable Rà 20-can be as simple as hydrogen atom or a carbon skeleton with functional groups attached Non-polar- hydrophobic Polar- hydrophillic Acidic- carboxyl group Base- amine side group · amino acids are joined together when a dehydration reactions removed a hydroxyl group from the carboxyl end of one amino acid and a hydrogen from the amino group of another à resulting covalent bond forms a peptide bond (*Note: repeating this process froms a polypeptide chain) - polypeptide- polymers of proteins - levels of stucture 1. primary- is the unique sequence of amino acids 2. secondary- coils and folds that result from the hydrogen bonds between the constituennts of the polypeptide backbone 3. tertiary- determined by interactions among various R groups 4. quarternary- results from the aggregation of two or more polypeptides
Protein Shape determines function - proteins can be globular or fibrous - pH, salt concentration, temperature, other factors can unravel/ dentature a protein - the folding of proteins is assisted by chaperonins
Protein Functions - structural support - storage - transport - cellular signaling - movement - defense against foreign substances - catalysts protein enzymes function as catalysts- regulating metabolism by selectively accelerating chemical reactions without being consumed
Nucleic Acids Store and Transmit Hereditary Information RNA- ribonucleic acid DNA- deoxyribonucleic
Nucleic Acids- polymers made of nucleotide monomers (3 parts: nitrogenous base, pentose sugar, phosphate group)
Nitogenous Bases:
Pyrimidines- CUT- Cytosine, tymine, uracel
Purine- Pure as Gold- Adenine, Guanine
Chapter 4: Carbon and the Molecular Diversity of Life (Checked at 9:00 PM 12/11/10. Ch 4 looks fine. Ch 5 only finished through lipids)Functional Groups
Aldehydes (if the carbonyl groups is at the end of the carbon skeleton)
Attracts water molecules,helping dissolve organic compounds such as sugars
The covalent bond between oxygen and hydrogen is so polar that hydrogen ions tend to dissociate reversibly
Can transfer energy between organic molecules
Pictures taken from Campbell Biology Online E-Book
Important Concepts
₪ Organic Chemistry – the study of carbon compounds
₪ Hydrocarbons – Organic moleclues that consist of only carbon and hydrogen atoms
₪ Tetravalence – The carbon completes its valence shell by sharing electrons with other atoms in four covalent bonds. This makes a large, complex molecule possible.
₪ Isomers – Compounds that have the same molecular formula but different structures.Therefore, they have different chemical properties.
o Structural Isomers – Molecules that have the same molecular formula but differ inthe covalent arrnagement of atoms
o Geometric Isomers – Compounds with the same covalent partnerships that differ in the spatial arrangement of atoms around a carbon-carbon double bond.
₪ Enantiomers – Molecules that are mirror images of each other
o Levo-Isomer: Left Handed
o Dextra-Isomer: Right Handed
₪ Living matter consists mainly of: Carbon, Oxygen, Hydrogen, Nitrogen, Sulfur, and Phosphorus
₪ Carbon (with its four covalent bonds) is the basiv building block in molecular architecture.
Chapter 5: The Structure and Function of Macromolecules
Overview-The Molecules of Life
- Each type of small molecule has unique properties from the arrangement of their atoms
- The four main classes of large biological molecules are: carbohydrates, lipids, proteins, and nucleic acids
5.1: Most Macromolecules are Polymers, built from Monomers
- Carbohydrates, proteins, and nucleic acids are chain like molecules called polymers
- A polymer is a long molecule with many similar or identical building blocks linked by a covalent bond.
- Smaller building blocks of a polymer is called a monomer
The Synthesis and Breakdown of Polymers
- Monomers are connected by a reaction in which two molecules are covalently bonded to each other through loss of a water molecule called condensation reaction (dehydration reaction) -- the molecule lost is water
- When a bond forms between two monomers each monomer contributes part of the water molecule that is lost--hydroxyl group (-OH) and hydrogen (-H)
- This process is repeated to form a polymer
- Cell must expend energy to have dehydration reactions and with the help of enzymes
- Polymers are broken down to monomers by hydrolysis - this process is essentially the reverse of dehydration reaction -- means to break with water
- Bonds between monomers are broken down by the addition of water molecules -- a hydrogen from the water attaching to one monomer and a hydroxyl group attaching to the adjacent monomer (Ex. digestion in our bodies)
The Diversity of Polymers
- Each cell has thousands of kinds of macromolecules -- varies between types of cells
- Difference between human siblings is in the variation in polymers -- DNA and proteins
- Monomers are constructed from 40-50 common monomers (Ex. proteins are made up of 20 different amino acids in a chain)
- Small molecules common to all organisms are ordered into unique macromolecules
5.2: Carbohydrates Serve as Fuel and Building Material
- Carbohydrates: include both sugars and polymers of sugars
- The simplest carbohydrates are monosaccharides (simple sugars) -- Disaccharides are double sugars -- two monosaccharides joined by condensation reaction
Sugars
- Monosaccharides have some multiple of unit CH2O
- Glucose is the most common monosaccharide -- central importance to the chemistry of life (know other examples such as fructose and galactose - not structure but names)
- Molecule has carbonyl group and multiple hydroxyl groups
- Glucose has ring formed - Know this
(from Figure 5.4 on Online Website)
- Monosaccharides are a major nutrient for cells
- Cellular respiration is when cells extract energy from glucose molecules
- Disaccharide is two monosaccharides joined by a glycosidic linkage - a covalent bond formed between two monosaccharides by dehydration reaction (sugar is a disaccharide-sucrose-with two monomers of glucose and fructose)
- Plants transport carbohydrates from leaves to roots
- Lactose is the sugar present in milk and is a disaccharide
- Polysaccharide are macromolecules with hundreds of monosaccharides jointed with glycosidic linkages.
- They serve as storage materials and building materials for structures that protect the cell and organisms
- Starch is a storage polysaccharide of plants- it is a polymer consisitng of entirely glucose monomers.
- Plants store starch within their chloroplast - it serves as cellular fuel and represents stored energy
- Animals store polysaccharides called glycogen- it is a polymer of glucose - stored mainly in the liver and muscle cells - hydrolysis of glycogen in these cells releases glucose when there is a demand for sugar
- Organisms build strong materials from structural polysaccharides - like cellulose - a major component of plant cell walls
- Cellulose is a polymer of glucose but has different glycosidic linkages
- Cellulose has a three dimensional shape but starh has a helical shape - cellulose is straight and never branches
- Many organisms do not have the enzyme needed to digest cellulose - humans do not - the cellulose passes through the digestive tract and is eliminated - the cellulose abrades the wall of the digestive tract and helps food pass through smoothly
- Chitin the carbohydrate used by arthropods to build their exoskeletons - hard case that surrounds the softer parts of an animal
- Chitin is similar to cellulose - the glucose monomer of chitin has a nitrogen-containing appendage.
5.3: Lipids are a Diverse Group of Hydrophobic Molecules
- Lipids are the molecules that do not consist of polymers
- Lipids are grouped together because they share one important shape: they have little to no affinity to water - hydrophobic - may have some polar bonds but most of lipids consist of hydrocarbons
- Fats are large molecules assembled from smaller molecules by dehydration reaction - constructed of glycerol and fatty acids
- A fatty acid has a long carbon skeleton (16-18 carbon atoms) - one end of fatty acid is carboxyl group (funtional group) - hydrocarbon chain is attached to carboxyl group ( reason it is hydrophobic)
- To make a fat three fatty acid molecules bind to glycerol by ester linakge (bond between a hydroxyl group and a carboxyl group) resulting fat is a triacylglycerol
- Fatty acids vary in length and location of the double bonds
- There are saturated and unsaturated fats - refers to the structure of the hydrocarbon chains of the fatty acids
- Saturated Fatty Acid - no double bonds between carbon atoms composing the chain - as many hydrogen atoms as possible bind to skeleton
- Unsaturated Fatty Acid - one or more double bond - formed by the removal of hydrogen atoms from teh carbon skeleton
- Most animal fats are saturated - lard and butter - solid at room temperature
- Plants and fish fats are unsaturated - liquid at room temperature - oils
- Saturated fats in excess in diet leads to cardiovascular diseases - atherosclerosis - build up impedes blood flow in blood vessels
- Major function of fats is energy storage - stores more than polysaccharides (starch) - useful for animals since they must carry their stored energy
- Phospolipid - similar to a fat - has only two fatty acids attached to a glycerol (instead of three)
- Hydrocarbon tails are hydrophobic and heads are hydrophilic - bilayer as boundry between cell and the external enviroment
- Steroids are lipids characterized by a carbon skeleton with four fused rings
- Cholesterol is a type of steroid that is common in animal cell membranes - crucial molecule in animals - synthesizes sex hormones
Chapter 5
organization is the key to life
protein- consists of one or more polypeptides folded and coiled into a specific conformation (end in –ase)
Protein Structure
- all proteins are constructed from the same set of 20 amino acid monomers, but The shape determines the function
- Amino Acids- organic molecules with both carboxyl and amino groups
· at the center is the alpha carbon with 4 components attached
1.
2. carboxyl group
3. amino group
4. variable Rà 20-can be as simple as hydrogen atom or a carbon skeleton with functional groups attached
Non-polar- hydrophobic
Polar- hydrophillic
Acidic- carboxyl group
Base- amine side group
· amino acids are joined together when a dehydration reactions removed a hydroxyl group from the carboxyl end of one amino acid and a hydrogen from the amino group of another à resulting covalent bond forms a peptide bond (*Note: repeating this process froms a polypeptide chain)
- polypeptide- polymers of proteins
- levels of stucture
1. primary- is the unique sequence of amino acids
2. secondary- coils and folds that result from the hydrogen bonds between the constituennts of the polypeptide backbone
3. tertiary- determined by interactions among various R groups
4. quarternary- results from the aggregation of two or more polypeptides
Protein Shape determines function
- proteins can be globular or fibrous
- pH, salt concentration, temperature, other factors can unravel/ dentature a protein
- the folding of proteins is assisted by chaperonins
Protein Functions
- structural support
- storage
- transport
- cellular signaling
- movement
- defense against foreign substances
- catalysts
protein enzymes function as catalysts- regulating metabolism by selectively accelerating chemical reactions without being consumed
Nucleic Acids Store and Transmit Hereditary Information
RNA- ribonucleic acid DNA- deoxyribonucleic
Nucleic Acids- polymers made of nucleotide monomers (3 parts: nitrogenous base, pentose sugar, phosphate group)
Nitogenous Bases:
Pyrimidines- CUT- Cytosine, tymine, uracel
Purine- Pure as Gold- Adenine, Guanine